Yami Yugi's Baby Boy
by Atarya QueenofEgypt
Summary: Grandpa is out of town with Yugi's mom and it's just the two brothers Yugi and Yami. (Cute fluff and puzzleshipping)
1. What's Wrong With Yugi?

**Author's Note:**

 **Hey, guys. I hope that you all are enjoying the Yu-Gi-Oh stories that I have made, along with CptTails as my co-writer and boyfriend. CptTails, I hope that we can continue. This is my first ever Yu-Gi-Oh yaoi story that I'm doing with Lover Of Yugioh Yaoi. I hope that you all enjoy it.**

It was an amazing spring day outside. The sun was shining, the flowers were blooming and the wind was blowing. Yugi looked out the window, in anticipation. School was just about to be let out for spring vacay. He was bouncing up and down.

Yami was sitting across from Yugi and his friends, watching him.

Yami smiled as he watched the other excited one, looking forward to being able to get up and walk over to him.

The whole time he was admiring how cute Yugi was as he stared out over the blooming flowers that were gently swaying in the wind.

Yugi stopped bouncing and looked over at his hikari.

 _Did I do something wrong?_ Yugi said to himself as he looked over at Yami, who was staring out the window.

He walked over to Yami, bouncing.

"Hi, Yami!" Yugi said, excitedly.

Yami smiled.

"Hey, my excited little one," Yami greeted. "What brings you over here?"

"I couldn't help but notice you feeling alone so, I came over here to help you not be alone." Yugi said, with a reassuring smile.

Yami smiled and pulled Yugi onto his lap, wrapping his arms around the smaller boy.

"I'm never alone when you're with me so I guess that means you have to sit here until school is over," Yami whispered to Yugi.

Yugi saw Tristan, Joey, Tea, Bakura and Duke playing a game of Duel monsters. They were having fun.

Yugi looked at Yami.

"Should we join them, Yami?" Yugi asked.

"I suppose so... providing that you stay by my side," Yami said, with a slight smirk.

Yugi giggled and began to hold Yami's hand.

He loved when Yami was like this. He was very grateful that Yami loved him and protected him, like a father.

"Yami, isn't this nice? We're about to play our favorite game of Duel monsters!" Yugi said, excited that Yami was right beside him.

"This is nice," Yami replied with a smile, hugging Yugi.

Yugi began to coo as they walked over to them.

Joey looked up at them.

"Hey, Yuge. Hi, Pharaoh." Joey said, looking at the two brothers.

Yugi looked at Joey.

"Hi, Joey." Yugi said.

"Hey, Joey. How's the games going?" Yami asked.

Joey looked at his deck.

"They're going good. Thank ya for asking." Joey said as he looked up from what he was doing to look at Yami.

Yugi was bouncing up and down.

Tea began to notice.

"Yami, is Yugi okay?" Tea asked, worried.

"He's fine. He's just a little over excited," Yami replied, with an amused chuckle.

Yugi looked at Yami, worried.

"What's wrong, Yugi?" Yami asked, with a frown.

Yugi's eyes began to bubble with tears.

He then ran out of the classroom.

"Yugi!" Tea said, worried.

Yami frowned worriedly and followed after the other boy, calling out for him.

Yugi was sitting in the hallway beside the classroom door.

He clutched onto his millennium puzzle.

"YAMI!" Yugi said, crying.

"What's wrong? Did I say something wrong?" Yami asked, worriedly as he ran over to the other boy, sitting down and hugging Yugi.

"Don't go, Yami. Please don't let go of me." Yugi said, worried.

"I won't let you go, Little One. I'll never let you go," Yami whispered soothingly as he gently rocked the smaller boy.

Yami could feel Yugi's heart beating faster.

Weevil Underwood and Rex Raptor were coming out of Mrs. Camp's English three class when they saw the two.

"Hey..." Weevil said.

"What do you two want?" Yami asked, slightly colder then he had intended.

"We were just wanting to check on the little bug." Weevil said as he was looking at Yugi.

"Don't call him a bug!" Yami growled angrily, tightening his arms slightly around Yugi.

Yugi was coughing.

Yami loosened his arms around the smaller boy, gently rubbing Yugi's back.

"Are you alright, little one?" Yami asked, worriedly.

Weevil and Rex kneeled down to Yugi's level.

Yugi wouldn't speak to Yami.

Yami glared at them and then he looked down at Yugi before he looked back at the other two.

"Have these two bakas hurt you, Yugi?" Yami asked, glaring at Rex and Weevil.

Yugi shook his head no and pointed at his throat.

Yami frowned and gently looked at Yugi's throat, trying to work out what was wrong with the younger boy.

"I think we need to take you to the nurse," Yami muttered.

"No..." Yugi said, talking in a normal voice.

"Do you know what's wrong then? I don't like when this happens," Yami said, softly.

"That big boy in gym class... Rafael... He hurt me..." Yugi said, in a nervous and scared voice.

"Where did he hit you?" Yami asked, trying to control his anger at the news.

Yugi pointed at his right arm and his throat.

Yami frowned and looked at the bruises.

 _I think I'll have to deal with the bastard later. Right now I have to stay with Yugi,_ Yami thought.

"Are you alright, Yugi? Can you breathe normally and still move your arm properly?" Yami asked, softly.

Yugi began to breathe in and out, normally.

Yugi then began to move his arm.

He cried out in pain.

"You're going to the nurse to make sure that he didn't harm your arm too seriously and that's final," Yami said, sternly as he picked Yugi up bridal style.

 **(Okay. So, Yugi's been acting weird since the beginning of the story. His mood has changed from happy to being in pain. What do you think that the Orichalcos guy did to Yugi? Please review and stay tuned for chapter two.)**


	2. A Broken Arm

**Author's Note:**

 **Hey. I'd like to thank DeformedStrawberry, Lover Of Yu-Gi-Oh Yaoi, PhantomBrat and Dragon-chan for following and favoriting me. I would like to see more reviews though. Anyways, I hope that you all enjoy chapter two and if you need a recap of what happened last chapter, here it is…**

~Flashback~

" _Do you know what's wrong then? I don't like when this happens," Yami said, softly._

 _"That big boy in gym class... Rafael... He hurt me..." Yugi said, in a nervous and scared voice._

 _"Where did he hit you?" Yami asked, trying to control his anger at the news._

 _Yugi pointed at his right arm and his throat._

 _Yami frowned and looked at the bruises._

 _I think I'll have to deal with the bastard later. Right now I have to stay with Yugi, Yami thought._

"Are you alright, Yugi? Can you breathe normally and still move your arm properly?" Yami asked, softly.

 _Yugi began to breathe in and out, normally._

Yugi then began to move his arm.

He cried out in pain.

 _"You're going to the nurse to make sure that he didn't harm your arm too seriously and that's final," Yami said, sternly as he picked Yugi up bridal style._

~End Flashback ~

Just as Yami was about to carry Yugi to the nurse, Tea opened the classroom door and came out.

"Pharaoh..." Tea said as she was walking out the door and to where they were.

Weevil and Rex snickered at Yugi and Yami.

Yami glared at Weevil and Rex.

"Yes, Tea?" Yami asked, turning to look at her so she knew she had his full attention.

"I'm a nurse..." Tea said.

It was true.

Tea was wanting to be a dancer and a nurse. She was great with kids.

Yami smiled.

"Just what I was looking for. Can you check Yugi's arm for me please?" Yami asked, kindly.

"My kit is in the classroom. Can you come with me please?" Tea said, in a firm voice.

Weevil and Rex looked at Yami.

"We would like to come too." Weevil said, in an innocent love voice.

"Why would you two want to come?" Yami asked, with a frown.

He disliked Weevil and Rex. They were liars and cheaters in Duelist Kingdom and they did not duel with honor.

"We love to watch Tea work in medical class." Weevil said, hearts in his eyes.

"And we also admire Yugi and you." Rex Raptor said.

Yami frowned and thought about it.

"Fine but stay out of Tea's way," Yami said sternly, following Tea.

"Do you want to know where Rafael is right now?" Weevil asked as they were going into the classroom.

"I'll kick his ass later once I know Yugi is alright," Yami replied. "So it would be pointless to know right now. Thanks anyway."

Just when they got into the classroom, Yugi was crying out in pain.

"Please make his pain go away," Yami pleaded to Tea as Yugi was crying.

Tea led the boys over to where Yugi sat at.

Yugi looked at Yami, wanting to hold his hand.

Yami sat on Yugi's chair with Yugi on his lap, holding Yugi's hand for comfort.

Joey looked at them as he was in his desk, sitting.

"What da hell happened to Yugi?" Joey asked,in an urgent voice, concerned for his best friend.

"Take his jacket off slowly." Tea instructed.

Yami frowned when Yugi tightened his hand on his.

"My hands are a little held up. Can one of you please remove his jacket for me?" Yami asked.

Joey began to remove Yugi's jacket slowly.

Yugi gripped onto Yami and cried.

"I don't get why Yugi's crying. What da hell happen to Yuge?" Joey said.

"Rafael was an asshole and did this to him," Yami replied for Yugi, gently stroking Yugi's back.

Tea took a look at Yugi's right arm.

"Bruises..." Tea said as she looked for any sign of broken bones.

With every little press, Yugi felt pain.

"Yami, it hurts..." Yugi said as tears were dripping down from his eyes.

"I know, Little One but, Tea needs to determine how severe your injury is," Yami said softly, feeling very bad that he couldn't do any more for Yugi.

Tea began to feel Yugi's elbow.

He cried out in pain.

"That's where the source of the pain is coming from." Tea said.

"Do you know what is causing his pain?" Yami asked, worriedly.

"I think it's the bruises or...there's an inflamed joint somewhere." Tea said as she began to bend Yugi's elbow.

Yugi cried louder.

"Yep. Just as I suspected..." Tea said as she began to get her medical bandages and tape out of her first aid kit.

"What did you suspect?" Yami asked. "Is it the inflamed joint thing you were mentioning?"

"Yes. It's his elbow." Tea said.

Joey and Tristan came over to them.

"It's going to be okay, buddy. We're here for you." Tristan said, comfortingly.

"All da way, Yuge." Joey said.

Tea gave Yugi a reassuring smile.

Yugi began to smile a little bit but, he was still in pain.

"Yami, do you know how to do a cast?" Tea asked Yami.

Yugi looked at Yami and cooed.

"I don't know. I think I can do it if someone refreshes my memory on what has to be done," Yami replied.

"It's like wrapping a present except that it doesn't have to be tight and just right." Tea said.

"Remember when Yugi was a dead Pharaoh for Halloween?" Joey said.

"He was wrapped up in toilet paper." Tristan said.

Yami nodded.

"I'll give it a go and you guys have to correct me if I'm wrong," Yami said.

Yugi began to relax and close his eyes.

Tea gave Yami the materials he needed.

"Thank you," Yami said as he took the material and set to work wrapping up Yugi's sore arm.

As Tea was watching Yami work, she realized that Yami was making a mistake as he was wrapping Yugi's arm.

"Yami, you're working on a cast, not a mummy." Tea said as she was now beginning to help him wrap Yugi's arm up in a cast and sling.

"I told you that I wasn't sure about this and that you may have to help me," Yami said, with a light blush as he continued to work with Tea's help.

 **(Okay. So, Tea's a nurse and Yami doesn't know what to do for his little Yugi. Yami is a 5,000 year old Pharaoh in Ancient Egypt who knows how to wrap up the dead. Please read and review and stay tuned for chapter three.)**


	3. Badass Rafael

A few minutes later, Yugi's cast and sling were done and Yugi began to wake up from his nap.

"Hey, Pharaoh. Yuge's waking up." Joey said, realizing.

Yami smiled.

"Good. How do you feel, Little One?" Yami asked as he wrapped his arms around Yugi's waist.

Yugi began to rub his eyes with his left hand but, couldn't do it.

Yami saw Yugi frown.

"What's wrong, Little One?" Yami asked.

"I can't rub the sleep from my eyes." Yugi said as he opened his eyes to look at Yami.

Yami smiled and gently rubbed Yugi's eyes from him.

"Why can't you rub your eyes?" Yami wondered as he tilted his head.

"My arms are sore." Yugi said, looking at Yami.

Yami frowned.

"Can you look at his arms, Tea?" Yami asked with worry in his voice.

Tea nodded and looked at both of Yugi's arms.

"All I see are bruises. Nothing more." Tea said, in observance.

"Then why can't he move his arms to rub his eyes?" Yami asked.

"They're just too sore." Tea said.

Yugi nodded his head yes and cooed.

Yami sighed and gently rubbed Yugi's arms, making sure not run his hands over the bruises.

"We should go pay dat creep a visit." Joey said, his fists drawn.

Yugi began to whimper.

"Later. We will deal with him when Yugi's a little better," Yami said, not wanting to leave Yugi when his arms are too sore to move.

"Yami, I'm scared..." Yugi said.

"Why? Is something wrong, Little One?" Yami asked.

"I'm scared that Rafael's going to hurt me again." Yugi said as he looked at Yami, worried.

"He won't hurt you again, Aibou. Me and the others will make sure of that," Yami promised.

Yugi looked at the door.

Yami looked in the direction that Yugi was looking.

"Did he threaten to beat you after class finished?" Yami asked, worriedly.

"He's in our class right now." Weevil said.

Yami narrowed his eyes.

"Joey, keep him away from us if you can please. I'll help if he becomes too difficult," Yami said. "Right now Yugi needs me here."

Joey nodded and went with Tristan, Weevil and Rex out the door.

"You won't be hurt by him. Joey, Tristan and our two mini shadows will protect you from Rafael," Yami whispered to Yugi, with a gentle smile.

Yugi looked at the clock.

It was 3:15 PM.

Just then, the bell began to ring.

"Ready to go home, Little One?" Yami asked with a smile.

Yugi looks down at his bag and tries to grab it.

Yugi looked at Yami.

"Yes, Yami. It's just... I can't get my bag." Yugi said as he was trying to reach.

Tea saw that he was struggling and bent down and picked it up and gave it to Yami.

"Thanks, Tea," Yami said with an appreciative smile, slinging the bag over his shoulder before he stood up with Yugi still in his arms.

Yugi looked at the door, worried.

"Don't worry, Aibou. He won't hurt you. You have the entire Yugi-tachi here to support you," Yami said, with a smile.

Yugi began to giggle.

Yami smiled brightly at the smaller boy and started walking out of the room with Tea following behind him.

Yugi began to hear Rafael's voice up the hallway towards the cafeteria.

Joey and Tristan came back.

"Hey, guys." Joey said.

Yugi began to cover his ears.

"Hey. Is everything alright down or there or do you need a hand?" Yami asked, gently rocking Yugi like a baby in an attempt to soothe the frightened teen.

Rafael was waiting for them.

He waved at Yami.

Yami glared at Rafael and placed Yugi down gently, placing him behind Tea before he readied himself to fight Rafael if he had to.

"What do you want, Rafael? Haven't you done enough already?" Yami growled angrily.

"Pharaoh, you wasn't there for Yugi. Not during gym class you wasn't." Rafael said.

Yugi began to scream.

"Cover Yugi's ears please, Tea," Yami said, before he turned back to Rafael with an even colder glare. "That was a mistake that will never happen again. Once Yugi is better I'll ensure that you regret the day you were born," Yami growled.

Yugi began to run to Mrs. Hunter's classroom.

Naomi used to be a scribe in Ancient Egypt to Yami but, now, she was an Egyptian history teacher.

She saw the little boy enter her classroom.

She was about as tall as Yugi was.

"Hi, Yugi. Are you alright?" Mrs. Hunter asked him.

Yugi's eyes were filled with tears.

Mrs. Hunter began to sit right next to him and comfort him.

"You miss the Pharaoh, don't you?" Mrs. Hunter asked him.

Yugi nodded his head yes.

Meanwhile...

"Look, Pharaoh. You're the one who gave Yugi up during the Orichalcos duel. I thought that I had gotten rid of you until I realized that you were hiding behind him all along." Rafael said.

"I didn't intentionally give Yugi up and I wasn't hiding behind him!" Yami snapped. "He pushed me out of the way and saved me. I had every intention to lose my soul for what I had done to my trusted friends."

"Yami..." Tea said, worried and started looking around for Yugi.

Yami looked around and sighed.

"He probably went to Mrs Hunter's class," Yami whispered to Tea, making sure that Rafael didn't hear him.

"Do you want me to come with you or do you want me to finish up here?" Yami asked as he was looking away from Rafael for a minute.

"Let's pick a fight with da big guy later." Joey said.

Yami nodded and glared at Rafael.

"Hurt Yugi again and I'll hurt you twice as much. Follow me now and I'll break your limbs into thousands of tiny pieces," Yami threatened before he turned and started walking towards where he knew Yugi would have gone.

Yugi was talking to Mrs. Hunter when Yami came in.

Mrs. Hunter turned around to him.

She curtsied.

"What can I do for you, Pharaoh?" Mrs. Hunter asked.

"We were just curious if Yugi was here after he disappeared on us. Are you alright, Yugi?" Yami asked with a smile, walking over and kneeling down in front of Yugi.

Yugi looked at Yami.

"I couldn't bear to see you two fighting again." Yugi said as he reached his hand out to Yami.

Yami smiled softly.

"I'll try not to fight with him unless he threatens you again," Yami said. "Does that make you feel better, Little One?"

"Yes, Yami." Yugi said.

"I knew that Rafael would strike...I'm sorry if I failed you, Pharaoh." Mrs. Hunter said as she was looking at the ancient hieroglyphs.

"It's alright, Naomi. Is there anything else in the near future that we should be aware of?" Yami asked.

Mrs. Hunter continued reading the ancient Egyptian hieroglyphs.

"Also, be aware of something that's going to happen when you two get home today." Mrs. Hunter said as she looked back at the two.

Yugi looked down at his pants.

"Any hints on what will happen?" Yami asked, with a worried frown. "Why are you looking at your pants, Aibou?"

Mrs. Hunter shrugged and looked at Yugi.

"He probably either has to go to the bathroom..." Tea began to say.

"Or he probably had an accident." Joey said.

Yami blushed lightly.

"Let's go, Yugi," Yami said, softly as he helped the other teen up, leading him towards the bathroom.

"But... But Yami... It's time to go home." Yugi said.

"Do you need the bathroom or do you want to go home?" Yami asked, softly. "I don't mind if you want to go home."

"G...Go home." Yugi said, nervously.

"Alrighty, Aibou. Let's grab our gear and then head home," Yami said, smiling warmly at Yugi.

Yugi tried to grab his bag but, couldn't.

Mrs. Hunter saw that Yugi was having trouble and she began to help him.

"Here, Pharaoh..." Mrs. Hunter said as she gave Yugi's bag to Yami and as she was giving it to him, something fell out of it.

It was a diaper.

Yugi blushed darkly and tried to pick the embarrassing item up but he couldn't.

Yami picked it up and shoved it back into Yugi's back, slinging the bag over his shoulder.

"Yami... I don't know what to do or how to hold your hand." Yugi said as he looked at his partner.

"It'll be alright, Aibou," Yami said, with a warm smile as he took Yugi's hand for Yugi, gently squeezing his hand comfortingly.

"Let's go home, Yami." Yugi said, with a smile.

"Sure thing," Yami said, kissing Yugi's forehead before he started leading his partner out of the classroom.

 **(So, Yami is very protective of Yugi, especially since Fate Of The Pharaoh episodes. Rafael is being a badass jerk, isn't he? Anyways, please read and review and stay tuned for chapter four.)**


	4. The Mark Of Spring Break

**Author's Note:**

 **Hey, guys. Glad that you all like and are enjoying Yami Yugi's Baby Boy so far. 5 favorites and 6 followers so far. I hope that I get more. Sorry if this is a late update. I'd like to thank Lover Of Yu-Gi-Oh Yaoi for being my co-writer and I would also like to thank CptTails for being my boyfriend. You're awesome and I love how you motivate me everyday. Anyways, here's the late update. If it's short, I'm sorry.**

~Flashback~

 _"But... But Yami... It's time to go home." Yugi said._

 _"Do you need the bathroom or do you want to go home?" Yami asked, softly. "I don't mind if you want to go home."_

 _"G...Go home." Yugi said, nervously._

 _"Alrighty, Aibou. Let's grab our gear and then head home," Yami said, smiling warmly at Yugi._

 _Yugi tried to grab his bag but, couldn't._

 _Mrs. Hunter saw that Yugi was having trouble and she began to help him._

 _"Here, Pharaoh..." Mrs. Hunter said as she gave Yugi's bag to Yami and as she was giving it to him, something fell out of it._

 _It was a diaper._

 _Yugi blushed darkly and tried to pick the embarrassing item up but he couldn't._

 _Yami picked it up and shoved it back into Yugi's back, slinging the bag over his shoulder._

 _"Yami... I don't know what to do or how to hold your hand." Yugi said as he looked at his partner._

 _"It'll be alright, Aibou," Yami said, with a warm smile as he took Yugi's hand for Yugi, gently squeezing his hand comfortingly._

 _"Let's go home, Yami." Yugi said, with a smile._

 _"Sure thing," Yami said, kissing Yugi's forehead before he started leading his partner out of the classroom._

~End flashback~

On the way home...

As the two were walking together, hand in hand, a question began to slip into his mind.

 _I didn't put the diaper in there this morning... How did it get there?_ Yugi said to himself as he was trying to figure it out.

Then, he looked at Yami, nervously.

"Yami?" Yugi said.

"Yes, Aibou?" Yami asked, smiling at Yugi kindly.

"Did you put that diaper in my bag?" Yugi asked, curiously.

Yami blushed lightly again.

"I don't know. I had a dream where I did but I didn't think I did in real life. I could have though," Yami said.

Yugi sighed sadly.

When they got to the Kame Game shop, they saw Grandpa with his bags.

"G-Grandpa?" Yugi said, worried.

Solomon Moto looked at his grandson.

"Yugi, what happened to your arm?" Solomon Moto asked.

Yugi looked at Yami with a look that said please tell him. I'm uncomfortable.

"He had a run in with Rafael at school. Rafael gave him several bruises and he currently can't use his arms. Where are you off to?" Yami asked with a frown.

Solomon Moto looked at his bags.

"I'm going to go see Yugi's mother." Solomon said.

Yugi looked at Yami and cooed.

"Are we staying here or do you want to go, Yugi?" Yami asked as he looked at his partner.

Then, Yami looked at the old man that had the same hair as Yugi and him both, except that he had gray hair.

"Can Yugi go if he wants to?" Yami asked Solomon.

"He can but, this is last day of school before spring break starts. It's his decision." Solomon Moto said as a blue SUV began to come up towards the shop.

"What do you want to do, Yugi?" Yami asked his partner. "It's your choice."

Yugi tightly hugged Yami.

"I want to stay with you." Yugi said as he looked up at Yami.

Yami smiled and hugged Yugi.

"Then we will stay here if that is alright," Yami said.

Solomon smiled.

"You two need brother time as it is." Solomon said as the blue SUV was now parked and a woman with short red hair and brown eyes came out of the SUV and was now walking over to where the three was.

"Yugi!" She said as she was running to him.

"Janice!" Solomon called out to her.

Yugi's mom began to hug Yugi.

"Yugi, your arm! Who did this to you?" Yugi's mom asked, worried.

"A boy at school named Rafael did this to him," Yami replied on Yugi's behalf, smiling kindly at Yugi.

"You are very kind to Yugi." Yugi's mom said as she grabbed Solomon's luggage.

"Thank you. Would you like me to put that in the car?" Yami asked, kindly.

Yugi began to cry.

Yugi's mom began to notice.

"What's wrong with my little man?" Yugi's mom asked.

Yugi wouldn't respond.

"Sorry, Yugi. Do you want me to stay here instead of leave to put the bag in the car?" Yami asked, softly.

"You... You can help my mom." Yugi said.  
Yami smiled.

"I'll be right back, Aibou," Yami promised, gently squeezing Yugi's hand before he went to help Yugi's mother with Solomon's bag.

Yugi sighed sadly and laid down on the sidewalk.

"Thank you so much, Yami." Yugi's mom said, thanking Yami as they were walking together towards the blue SUV.

"No problem," Yami replied with a smile.

Yugi began to close his eyes.

Yugi's mom helped Solomon into the van.

"Take care of Yugi for us." Yugi's mother said as she was just about to pull out.

"I will," Yami promised as he waved to the departing family members.

Solomon and Yugi's mom winked at them one more time before they left.

Yami blushed before he turned around and walked over to Yugi, scooping the smaller teen up, bridal style and carrying him towards the house.

 **(This was a very good chapter. I'm sorry if they didn't give us enough on what Yugi's mother is named. She's known as Mrs. Moto but, I wasn't for sure what her first name was so, I took a guess at it. Anyways, I'm sorry if this chapter is kind of short but, I hope that you love chapter five. Please read and review. Thanks.)**


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